Multi-contrast imaging and digital refocusing on a mobile microscope with a domed LED array

We demonstrate the design and application of an add-on device for improving the diagnostic and research capabilities of CellScope--a low-cost, smartphone-based point-of-care microscope. We replace the single LED illumination of the original CellScope with a programmable domed LED array. By leveraging recent advances in computational illumination, this new device enables simultaneous multi-contrast imaging with brightfield, darkfield, and phase imaging modes. Further, we scan through illumination angles to capture lightfield datasets, which can be used to recover 3D intensity and phase images without any hardware changes. This digital refocusing procedure can be used for either 3D imaging or software-only focus correction, reducing the need for precise mechanical focusing during field experiments. All acquisition and processing is performed on the mobile phone and controlled through a smartphone application, making the computational microscope compact and portable. Using multiple samples and different objective magnifications, we demonstrate that the performance of our device is comparable to that of a commercial microscope. This unique device platform extends the field imaging capabilities of CellScope, opening up new clinical and research possibilities

Practical Implementation of Log-Scale Active Illumination Microscopy

Active illumination microscopy (AIM) is a method of redistributing dynamic range in a scanning microscope using real-time feedback to control illumination power on a sub-pixel time scale. We describe and demonstrate a fully integrated instrument that performs both feedback and image reconstruction. The image is reconstructed on a logarithmic scale to accommodate the dynamic range benefits of AIM in a single output channel. A theoretical and computational analysis of the influence of noise on active illumination feedback is presented, along with imaging examples illustrating the benefits of AIM. While AIM is applicable to any type of scanning microscope, we apply it here specifically to two-photon microscopy.National Institutes of Healt

Computational illumination for high-speed in vitro Fourier ptychographic microscopy

We demonstrate a new computational illumination technique that achieves large space-bandwidth-time product, for quantitative phase imaging of unstained live samples in vitro. Microscope lenses can have either large field of view (FOV) or high resolution, not both. Fourier ptychographic microscopy (FPM) is a new computational imaging technique that circumvents this limit by fusing information from multiple images taken with different illumination angles. The result is a gigapixel-scale image having both wide FOV and high resolution, i.e. large space-bandwidth product (SBP). FPM has enormous potential for revolutionizing microscopy and has already found application in digital pathology. However, it suffers from long acquisition times (on the order of minutes), limiting throughput. Faster capture times would not only improve imaging speed, but also allow studies of live samples, where motion artifacts degrade results. In contrast to fixed (e.g. pathology) slides, live samples are continuously evolving at various spatial and temporal scales. Here, we present a new source coding scheme, along with real-time hardware control, to achieve 0.8 NA resolution across a 4x FOV with sub-second capture times. We propose an improved algorithm and new initialization scheme, which allow robust phase reconstruction over long time-lapse experiments. We present the first FPM results for both growing and confluent in vitro cell cultures, capturing videos of subcellular dynamical phenomena in popular cell lines undergoing division and migration. Our method opens up FPM to applications with live samples, for observing rare events in both space and time

Computational structured illumination for high-content fluorescent and phase microscopy

High-content biological microscopy targets high-resolution imaging across large fields-of-view (FOVs). Recent works have demonstrated that computational imaging can provide efficient solutions for high-content microscopy. Here, we use speckle structured illumination microscopy (SIM) as a robust and cost-effective solution for high-content fluorescence microscopy with simultaneous high-content quantitative phase (QP). This multi-modal compatibility is essential for studies requiring cross-correlative biological analysis. Our method uses laterally-translated Scotch tape to generate high-resolution speckle illumination patterns across a large FOV. Custom optimization algorithms then jointly reconstruct the sample's super-resolution fluorescent (incoherent) and QP (coherent) distributions, while digitally correcting for system imperfections such as unknown speckle illumination patterns, system aberrations and pattern translations. Beyond previous linear SIM works, we achieve resolution gains of 4x the objective's diffraction-limited native resolution, resulting in 700 nm fluorescence and 1.2 um QP resolution, across a FOV of 2x2.7 mm^2, giving a space-bandwidth product (SBP) of 60 megapixels

On polymorphic logical gates in sub-excitable chemical medium

In a sub-excitable light-sensitive Belousov-Zhabotinsky chemical medium an asymmetric disturbance causes the formation of localized traveling wave-fragments. Under the right conditions these wave-fragment can conserve their shape and velocity vectors for extended time periods. The size and life span of a fragment depend on the illumination level of the medium. When two or more wave-fragments collide they annihilate or merge into a new wave-fragment. In computer simulations based on the Oregonator model we demonstrate that the outcomes of inter-fragment collisions can be controlled by varying the illumination level applied to the medium. We interpret these wave-fragments as values of Boolean variables and design collision-based polymorphic logical gates. The gate implements operation XNOR for low illumination, and it acts as NOR gate for high illumination. As a NOR gate is a universal gate then we are able to demonstrate that a simulated light sensitive BZ medium exhibits computational universality

MarsLux: HI-Resolution Illumination Maps Generator for Mars

Illumination simulation codes for the Moon's surface have been thoroughly developed during the last years. Despite works done for the Moon, no studies have investigated the relation between sunlight illumination and the Martian surface applying those codes done for the Moon to Mars. The objective of this work is to describe the development of a surface illumination simulation code, called MarsLux, which allows users to make a detailed investigation of the illumination conditions on Mars, based on its topography and the relative position of the Sun. Our code can derive accurate illumination maps, form topographic data, showing areas that are fully illuminated, areas in total shadow, and areas with partial shade, in short computational times. Although the code does not take into account any atmospheric effect, the results proved to be of high accuracy. The maps generated are useful for geomorphological studies, to study gullies, thermal weathering, or mass wasting processes as well as for producing energy budget maps for future exploration missions.Fil: Spagnuolo, Mauro Gabriel. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Ciudad Universitaria. Instituto de Estudios Andinos "Don Pablo Groeber". Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Instituto de Estudios Andinos "Don Pablo Groeber"; ArgentinaFil: Carballo, Federico Daniel. Servicio Geologico Minero Argentino; ArgentinaFil: Marco Figuera, R.. Jacobs University Bremen; AlemaniaFil: Rossi, A. P.. Jacobs University Bremen; Alemani